25IJ | pdb_000025ij

Cryo-EM structure of human Nav1.6 in complex with delta-paraponeritoxin-Pc1a

PDB DOI: https://doi.org/10.2210/pdb25IJ/pdb
EM Map EMD-80135: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Paraponera clavata
Expression System: Homo sapiens, synthetic construct
Mutation(s): Yes

Deposited: 2026-04-06 Released: 2026-05-20
Deposition Author(s): Yang, L., Fan, X., Huang, J., Yan, N.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 25IJ

This is version 1.0 of the entry. See complete history.

Literature

Diverse binding poses of gating modifier neurotoxins as agonists of human Nav1.6

Fan, X., Jian, H., Yang, L., Chen, J., Wang, H., Huang, X., Geng, J., Wu, Q., Xie, Y., Lu, F., Guo, Q., Shen, Z., Jin, X., Yan, N.

To be published.

Macromolecule Content

Total Structure Weight: 255.23 kDa
Atom Count: 12,227
Modeled Residue Count: 1,458
Deposited Residue Count: 2,179
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium channel protein type 8 subunit alpha	A	1,980	Homo sapiens	Mutation(s): 0 Gene Names: SCN8A, MED
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQD0 (Homo sapiens) Explore Q9UQD0 Go to UniProtKB: Q9UQD0
PHAROS: Q9UQD0 GTEx: ENSG00000196876
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UQD0
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A	Go to GlyGen: Q9UQD0-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Delta-paraponeritoxin-Pc1a	B	26	Paraponera clavata	Mutation(s): 1
UniProt
Find proteins for P41736 (Paraponera clavata) Explore P41736 Go to UniProtKB: P41736
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41736
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium channel regulatory subunit beta-1	C	173	Homo sapiens	Mutation(s): 0 Gene Names: SCN1B
UniProt & NIH Common Fund Data Resources
Find proteins for Q07699 (Homo sapiens) Explore Q07699 Go to UniProtKB: Q07699
PHAROS: Q07699 GTEx: ENSG00000105711
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q07699
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C	Go to GlyGen: Q07699-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	9		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth F]	2		N-Glycosylation	Interactions Focus chain E [auth F] Interactions & Density Focus chain E [auth F]

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PCW Query on PCW Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A]	K [auth A], N [auth A], O [auth A]	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₅ N O₈ P SNKAWJBJQDLSFF-NVKMUCNASA-O		Interactions Focus chain K [auth A] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain K [auth A] Focus chain N [auth A] Focus chain O [auth A]
9Z9 Query on 9Z9 Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en C₃₄ H₅₆ O₅ CEEBZAXXSRFQIC-GZSGZGDASA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
Y01 Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	L [auth A], M [auth A]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain L [auth A] Focus chain M [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	F [auth A], G [auth A], H [auth A], I [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-20

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32330052, 32322039, 32271252, and 32501082

Revision History (Full details and data files)

Version 1.0: 2026-05-20
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.